94 records Biopython Tutorial and Cookbook. Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock. Last Update. Biopython Examples. 1. Getting started. import Bio from import Seq dna = Seq(“ACGTTGCAC”) print(dna). (alternative). from et import IUPAC. The command print(len(dna)) displays the length of the sequence. Replacing records by records results in a different sequence record. Replacing.
|Published (Last):||12 July 2010|
|PDF File Size:||9.22 Mb|
|ePub File Size:||12.34 Mb|
|Price:||Free* [*Free Regsitration Required]|
The Biopython Project is an international association of developers of freely available Python https: Python is an object oriented, interpreted, flexible language that is becoming increasingly popular for scientific computing.
The Biopython web site http: Basically, the goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes. Basically, we just like to program in Python and want to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and scripts. All of the installation information for Biopython was separated from this document to make it easier to keep updated.
The short version is go to our downloads page http: Biopython runs on many platforms Windows, Mac, and on the various flavors of Linux and Unix. For Windows we provide pre-compiled click-and-run installers, while for Unix and other operating systems you must install from source as described in the included README file.
This is usually as simple as the standard commands:. You can in fact skip the build and test, and go straight to the install — but its better to make sure everything seems to be working.
The longer version of our installation instructions covers installation of Python, Biopython dependencies and Biopython itself. It is available in PDF http: Under Python 3 you must write:. Surprisingly that will also work on Python 2 — but only for simple examples printing one thing. In general you need to add this magic line to the start of your Python scripts to use the print function under Python 2.
This naming was used until June in the run-up to Biopython 1. If you still need to support old versions of Biopython, use these explicit forms to avoid problems. For more general questions, the Python FAQ pages https: This section is designed to get you started quickly with Biopython, and to give a general overview of what is available and how to use it. All of the examples in this section assume that you have some general working knowledge of Python, and that you have successfully installed Biopython on your system.
If you think you need to brush up on your Python, the main Python web site provides quite a bit of free documentation to get started with https: Since much biological work on the computer involves connecting with databases on the internet, some of the examples will also require a working internet connection in order to run.
In general this means that you will need to have at least some programming experience in Python, of course! However, this can also be a real benefit because it gives you lots of flexibility and control over the libraries. The tutorial helps to show you the common or easy ways to do things so that you can just make things work. What we have here is a sequence object with a generic alphabet – reflecting the fact we have not specified if this is a DNA or protein sequence okay, a protein with a lot of Alanines, Glycines, Cysteines and Threonines!
In addition to having an alphabet, the Seq object differs from the Python string in the methods it supports. The next most important class is the SeqRecord or Sequence Record. This holds a sequence as a Seq object with additional annotation including an identifier, name and description.
This covers the basic features and uses of the Biopython sequence class. Of course, orchids are not only beautiful to look at, they are also extremely interesting for people studying evolution and systematics. After a little bit of reading up we discover that the Lady Slipper Orchids are in the Orchidaceae family and the Cypripedioideae sub-family and are made up of 5 genera: CypripediumPaphiopedilumPhragmipediumSelenipedium and Mexipedium.
That gives us enough to get started delving for more information. A large part of much bioinformatics work involves dealing with the many types of file formats designed to hold biological data. These files are loaded with interesting biological data, and a special challenge is parsing these files into a format so that you can manipulate them with some kind of programming language. However the task of parsing these files can be frustrated by the fact that the formats can change quite regularly, and that formats may contain small subtleties which can break even the most well designed parsers.
We are now going to briefly introduce the Bio. Now try this in Python:. Biopython has a lot of parsers, and each has its own little special niches based on the sequence format it is parsing and all of that. AlignIO for sequence alignments. While the most popular file formats have parsers integrated into Bio.
AlignIOfor some of the rarer and unloved file formats there is either no parser at all, or an old parser which has not been linked in yet. Please also check the wiki pages http: The wiki pages should include an up to date list of supported file types, and some additional examples. One of the very common things that you need to do in bioinformatics is extract information from biological databases.
It can be quite tedious to access these databases manually, especially if you have a lot of repetitive work to do. Biopython attempts to save you time and energy by making some on-line databases available from Python scripts. Currently, Biopython has code to extract information from the following databases:. The code in these modules basically makes it easy to write Python code that interact with the CGI scripts on these pages, so that you can get results in an easy to deal with format.
In some cases, the results can be tightly integrated with the Biopython parsers to make it even easier to extract information.
First Steps in Biopython
The best thing to do now is finish reading this tutorial, and then if you want start snooping around in the source code, and looking at the automatically generated documentation. This will not only help us answer your question, it will also allow us to improve the documentation so it can help the tktorial person do what you want to do.
There are two important differences between Seq objects and standard Python strings. First of all, they have tutorual methods.
The alphabet object is perhaps the important thing that makes the Seq object more than just a string. The currently available alphabets for Biopython are defined in the Bio.
The advantages of having an alphabet class are two fold. First, this gives an idea tutotial the type of information the Seq object contains. Secondly, this provides a means of constraining the information, as a means of type checking. You can create an ambiguous sequence with the default generic alphabet like this:. However, where possible you should specify the alphabet explicitly when creating your sequence objects – in this case an unambiguous DNA alphabet object:.
Biopython Tutorial and Cookbook
In many ways, we can deal with Seq objects as if they were normal Python strings, for example getting the length, or iterating over the elements:. You can access elements of the sequence in the same way as tutorrial strings but remember, Python counts from zero! The Seq object has a. Note that this means that like a Python string, this gives a non-overlapping count:.
Biopython Examples · Biopython Tutorial
For some biological uses, you may actually want an overlapping count i. When searching for single letters, this makes no difference:.
SeqUtils module has several GC functions already built. Tutirial that using the Bio. GC function should automatically cope with mixed case sequences and the ambiguous nucleotide S which means G or C. Two things are interesting tutirial note. First, this follows the normal conventions for Python strings.
So the first element of the sequence is 0 which is normal for computer science, but not so normal for biology. When you do a slice the first item is included i. The main goal is to stay consistent with what Python does. The second thing to notice is that the slice is performed on the sequence data string, but the new object produced is another Seq object which retains the alphabet information from the original Seq object. Also like a Python string, you can do slices with a start, biopgthon and stride the step size, which defaults to one.
For example, we can get the first, second and third codon positions of this DNA sequence:. Another stride trick you might have seen with a Python string is the use of a -1 stride to reverse the string. You can do this with a Seq object too:. If you really do just need a plain string, for example to write to a file, or insert into a database, then biopythonn is very easy to get:.
Buopython does this automatically in the print biopythkn and the print statement under Python Naturally, you can in principle add any two Seq objects together – just like you can with Python strings to concatenate them.
Or, a more elegant approach is to the use built in sum function with its optional start value argument which otherwise defaults to zero:. Unlike the Python string, the Biopython Seq does thtorial currently have a. Python strings have very useful upper and lower methods for changing the case.
As of Biopython 1.
For nucleotide sequences, you can easily obtain the complement or reverse complement of a Seq object using its built-in methods:. As mentioned earlier, an easy way to just reverse a Seq object or a Python string is slice it with -1 step:. In all of these operations, the alphabet property is maintained. This is very useful in case you accidentally end up trying tugorial do something weird like take the reverse complement of a protein sequence:.
Before talking about transcription, I want to try to clarify the strand issue. Consider the following made up stretch of double stranded DNA which encodes a short peptide:. If you do want to do a true biological transcription starting with the template strand, then this becomes a two-step process:. For older releases you would have to use the Titorial.
You should notice in the above protein sequences that in addition to the end stop character, there is an internal stop as well. This was a deliberate choice of example, as it gives an excuse to talk about some optional arguments, including different translation tables Genetic Codes.